diff --git a/CHANGELOG.md b/CHANGELOG.md
index a068c06..e302bc1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,14 @@ All notable changes to Diskern are documented here. The format follows
 
 ## [Unreleased]
 
+### Fixed
+
+- A relative scan root no longer hides every finding a root-anchored rule
+  would have made. `diskern scan tmp` from `/var` reported nothing to
+  clean; roots are resolved to absolute paths before the walk
+- Scanning a root inside an excluded directory says so, instead of walking
+  it to an empty report that reads like a clean disk
+
 ## [0.2.0] — 2026-09-07
 
 ### Added
diff --git a/crates/diskern-cli/tests/relative_root.rs b/crates/diskern-cli/tests/relative_root.rs
new file mode 100644
index 0000000..133420d
--- /dev/null
+++ b/crates/diskern-cli/tests/relative_root.rs
@@ -0,0 +1,81 @@
+//! Issue #103. A relative scan root produced entries no anchored rule could
+//! match, so the scan reported nothing to clean for a directory full of
+//! matches. Driving the real binary with a working directory is the only
+//! honest way to pin this: changing the current directory inside a test would
+//! race every other test in the same binary.
+//!
+//! Unix only, and gated at the module level so the imports go with it:
+//! Windows paths normalize to `c:/...`, so a `/`-anchored pattern cannot
+//! match there and neither can the bug. Gating each item instead left these
+//! imports unused on Windows, which is four errors under the `-D warnings`
+//! clippy run CONTRIBUTING asks for.
+#![cfg(unix)]
+
+use serde_json::json;
+use std::fs;
+use std::process::Command;
+use tempfile::tempdir;
+
+/// A rule anchored at the filesystem root, like the shipped `/tmp/**` and
+/// `/var/log/**`.
+fn write_anchored_rules(path: &std::path::Path) {
+    let rules = json!({
+        "version": 1,
+        "rules": [{
+            "id": "anchored-marker",
+            "patterns": ["/**/*.marker"],
+            "category": "temp_file",
+            "verdict": "review",
+            "description": "Anchored rule for the relative-root regression."
+        }]
+    });
+    fs::write(path, serde_json::to_vec(&rules).unwrap()).unwrap();
+}
+
+#[test]
+fn a_relative_root_still_reaches_anchored_rules() {
+    let root = tempdir().unwrap();
+    fs::write(root.path().join("scratch.marker"), b"temp").unwrap();
+    let rules = root.path().join("rules.json");
+    write_anchored_rules(&rules);
+
+    // "." as the root, resolved against the child's working directory.
+    let output = Command::new(env!("CARGO_BIN_EXE_diskern"))
+        .current_dir(root.path())
+        .args(["scan", ".", "--rules", "rules.json", "--top", "0"])
+        .output()
+        .expect("diskern should start");
+
+    assert!(
+        output.status.success(),
+        "{}",
+        String::from_utf8_lossy(&output.stderr)
+    );
+    let stdout = String::from_utf8_lossy(&output.stdout);
+    assert!(stdout.contains("matched rule anchored-marker"), "{stdout}");
+    // The printed path is the one the manifest would record on quarantine.
+    assert!(stdout.contains("/scratch.marker"), "{stdout}");
+}
+
+#[test]
+fn an_absolute_root_reaches_the_same_rule() {
+    let root = tempdir().unwrap();
+    fs::write(root.path().join("scratch.marker"), b"temp").unwrap();
+    let rules = root.path().join("rules.json");
+    write_anchored_rules(&rules);
+
+    let output = Command::new(env!("CARGO_BIN_EXE_diskern"))
+        .args([
+            "scan",
+            &root.path().to_string_lossy(),
+            "--rules",
+            &rules.to_string_lossy(),
+            "--top",
+            "0",
+        ])
+        .output()
+        .expect("diskern should start");
+
+    let stdout = String::from_utf8_lossy(&output.stdout);
+    assert!(stdout.contains("matched rule anchored-marker"), "{stdout}");
+}
diff --git a/crates/diskern-core/src/lib.rs b/crates/diskern-core/src/lib.rs
index 25a5013..3f105b0 100644
--- a/crates/diskern-core/src/lib.rs
+++ b/crates/diskern-core/src/lib.rs
@@ -107,6 +107,8 @@ pub enum GenomeError {
         #[source]
         source: std::io::Error,
     },
+    #[error("scan root {path} is inside excluded directory {exclude}")]
+    ExcludedRoot { path: PathBuf, exclude: String },
     #[error("scan cancelled")]
     Cancelled,
     #[error("rules database error: {0}")]
diff --git a/crates/diskern-core/src/scanner.rs b/crates/diskern-core/src/scanner.rs
index 3646117..b67a237 100644
--- a/crates/diskern-core/src/scanner.rs
+++ b/crates/diskern-core/src/scanner.rs
@@ -63,25 +63,74 @@ impl ScanProgress {
 /// so the UI can render results while the scan runs.
 pub fn scan(opts: &ScanOptions, progress: Arc<ScanProgress>) -> Result<Vec<FileEntry>> {
     let mut out = Vec::new();
+    // Normalized once for the whole scan: the exclude list never changes, and
+    // both the root check below and every directory the walk opens use it.
+    let excludes: Vec<String> = opts.excludes.iter().map(|e| normalize_exclude(e)).collect();
 
     for root in &opts.roots {
         if progress.cancelled.load(Ordering::Relaxed) {
             return Err(crate::GenomeError::Cancelled);
         }
-        walk_root(root, opts, &progress, &mut out)?;
+        let root = absolute_root(root)?;
+        // Say so, rather than walking a root whose every entry the exclude
+        // list will drop. `/run/user/<uid>` holds real caches and sits under
+        // the `/run` exclude, so this is reachable — and an empty report is
+        // indistinguishable from a clean disk, which is the answer issue #103
+        // and #82 are both about not giving.
+        if let Some(exclude) = excluded_by(&root, &excludes) {
+            return Err(crate::GenomeError::ExcludedRoot {
+                path: root,
+                exclude: exclude.to_string(),
+            });
+        }
+        walk_root(&root, &excludes, opts, &progress, &mut out)?;
     }
     Ok(out)
 }
 
+/// Which exclude, if any, contains `path`.
+fn excluded_by<'a>(path: &Path, excludes: &'a [String]) -> Option<&'a str> {
+    let path = path.to_string_lossy();
+    excludes
+        .iter()
+        .find(|ex| is_within(&path, ex))
+        .map(String::as_str)
+}
+
+/// Issue #103. The rules are written against absolute paths, and the ones
+/// anchored at the filesystem root — `/tmp/**`, `/var/log/**` — are anchored
+/// on purpose: that is what keeps `/tmp` out of `~/tmp`. `jwalk` builds every
+/// entry's path from the root as it was handed in, so `diskern scan tmp` from
+/// `/var` produced `tmp/systemd-private/x`, which no anchored pattern can
+/// match. The walk found the files and the rules could not tell where they
+/// were, so the scan reported nothing to clean.
+///
+/// `absolute`, not `canonicalize`: it touches no filesystem, works on a path
+/// that does not exist, and leaves symlinks alone. `canonicalize` would
+/// rewrite `/var/tmp` to `/private/var/tmp` on macOS, scanning somewhere
+/// other than what was asked for.
+///
+/// It resolves a leading `.` but leaves `..` in place, since `a/../b` is only
+/// `b` when `a` isn't a symlink. A root spelled with `..` therefore still
+/// misses anchored rules; making it absolute is what the rules need, and
+/// guessing past a symlink is not.
+fn absolute_root(root: &Path) -> Result<PathBuf> {
+    std::path::absolute(root).map_err(|source| crate::GenomeError::Io {
+        path: root.to_path_buf(),
+        source,
+    })
+}
+
 fn walk_root(
     root: &Path,
+    excludes: &[String],
     opts: &ScanOptions,
     progress: &ScanProgress,
     out: &mut Vec<FileEntry>,
 ) -> Result<()> {
-    // Normalized once, not per directory: `process_read_dir` runs on every
-    // directory the walk opens, and the exclude list never changes.
-    let excludes: Vec<String> = opts.excludes.iter().map(|e| normalize_exclude(e)).collect();
+    // `process_read_dir` runs on every directory the walk opens, so the list
+    // arrives already normalized rather than being rebuilt here.
+    let excludes = excludes.to_vec();
 
     let walker = jwalk::WalkDir::new(root)
         .follow_links(opts.follow_symlinks)
@@ -275,6 +324,83 @@ mod tests {
         );
     }
 
+    /// Issue #103. Anchored rules only match absolute paths, so a relative
+    /// root has to be resolved before the walk, not after.
+    #[test]
+    fn a_relative_root_is_made_absolute() {
+        let cwd = std::env::current_dir().unwrap();
+        assert_eq!(absolute_root(Path::new("tmp")).unwrap(), cwd.join("tmp"));
+        assert_eq!(absolute_root(Path::new(".")).unwrap(), cwd);
+    }
+
+    /// An absolute root is already what the rules expect and must survive
+    /// untouched — in particular `/var/tmp` must not become the symlink
+    /// target `/private/var/tmp` that `canonicalize` would produce on macOS.
+    #[cfg(unix)]
+    #[test]
+    fn an_absolute_root_is_left_alone() {
+        let root = Path::new("/var/tmp");
+        assert_eq!(absolute_root(root).unwrap(), root);
+    }
+
+    /// The same guarantee on Windows, where it needs a different path to
+    /// state. `/var/tmp` is not absolute there — it is rooted but has no
+    /// drive, so `absolute` resolves it against the current one, which is
+    /// the right answer and not the one this test is about.
+    #[cfg(windows)]
+    #[test]
+    fn an_absolute_root_is_left_alone() {
+        let root = Path::new(r"C:\Users\example\AppData\Local\Temp");
+        assert_eq!(absolute_root(root).unwrap(), root);
+    }
+
+    /// A root the exclude list covers is an error, not an empty scan. The
+    /// walk would drop every entry and the report would look like a clean
+    /// disk, which is the answer #103 exists to stop giving.
+    #[test]
+    fn a_root_inside_an_exclude_is_refused() {
+        let dir = tempfile::tempdir().unwrap();
+        std::fs::write(dir.path().join("a.bin"), b"x").unwrap();
+
+        let err = scan(
+            &ScanOptions {
+                roots: vec![dir.path().to_path_buf()],
+                excludes: vec![dir.path().to_string_lossy().into_owned()],
+                ..Default::default()
+            },
+            Arc::new(ScanProgress::default()),
+        )
+        .unwrap_err();
+
+        assert!(
+            matches!(err, crate::GenomeError::ExcludedRoot { .. }),
+            "{err:?}"
+        );
+        assert!(err.to_string().contains("excluded directory"), "{err}");
+    }
+
+    /// The check is about containment, not a shared prefix: `/runtime-data`
+    /// is not inside `/run`, the same property `is_within` is written for.
+    #[test]
+    fn a_root_merely_sharing_a_prefix_with_an_exclude_is_scanned() {
+        let dir = tempfile::tempdir().unwrap();
+        let root = dir.path().join("runtime-data");
+        std::fs::create_dir_all(&root).unwrap();
+        std::fs::write(root.join("a.bin"), b"x").unwrap();
+
+        let entries = scan(
+            &ScanOptions {
+                roots: vec![root],
+                excludes: vec![dir.path().join("run").to_string_lossy().into_owned()],
+                ..Default::default()
+            },
+            Arc::new(ScanProgress::default()),
+        )
+        .unwrap();
+
+        assert_eq!(entries.len(), 1);
+    }
+
     #[test]
     fn scans_a_temp_tree() {
         let dir = tempfile::tempdir().unwrap();