diff --git a/src/execute.cc b/src/execute.cc
index 73464d1cb..d5ef8af73 100644
--- a/src/execute.cc
+++ b/src/execute.cc
@@ -150,7 +150,7 @@ bool AUTOQ::Automata<Symbol>::execute(const char *filename, std::vector<int> qub
             if (it == kRegexEnd)
                 THROW_AUTOQ_ERROR("Expected measure assignment (var = measure ...[n]) in \"" + line + "\".");
             std::string result = it->str(1);
-            int pos = 1 + atoi(it->str(2).c_str());
+            int pos = 1 + qubit_permutation[atoi(it->str(2).c_str())]; // the automaton level of the qubit, as for gates
             var_is_measure_what_qubit[result] = pos;
             // TODO: Actually, we should split the automaton here into two separate copies which
             // are produced from the measurement outcome of 0 and 1, respectively. However, we do
diff --git a/unit_tests/explicit_tree_aut_test.cc b/unit_tests/explicit_tree_aut_test.cc
index 50124d9d0..2af06d837 100644
--- a/unit_tests/explicit_tree_aut_test.cc
+++ b/unit_tests/explicit_tree_aut_test.cc
@@ -324,6 +324,28 @@ BOOST_AUTO_TEST_CASE(for_loop_summarization_complex_amplitudes){
     }
 }
 
+// `r = measure q[k];` must guard on the same automaton level that gates use for
+// q[k], also when the .hsl files reorder the qubits (#26).
+BOOST_AUTO_TEST_CASE(measurement_guard_uses_qubit_permutation){
+    std::string folder = test_dir_from_file(__FILE__, "testcase/MeasurePermutation/");
+    // {|sts>} and {|s0s>} put the two `s` qubits next to each other, so q[1] and q[2] swap levels.
+    const std::vector<std::pair<std::string, bool>> cases = {
+        {"if_reset.qasm", true},
+        {"if_wrong_qubit.qasm", false},
+        {"while_reset.qasm", true},
+    };
+    for (const auto& [circuit, expected] : cases) {
+        auto [autVec, qp] = AUTOQ::Parsing::TimbukParser<AUTOQ::Symbol::Concrete>::ReadTwoAutomata(folder + "pre.hsl", folder + "post.hsl", folder + circuit);
+        BOOST_REQUIRE_MESSAGE((qp == std::vector<int>{0, 2, 1}), circuit + ": the qubits are not reordered");
+        auto aut = autVec.at(0);
+        auto spec = autVec.at(1);
+        autVec.erase(autVec.begin(), autVec.begin() + 2);
+        bool verify = aut.execute(folder + circuit, qp, autVec);
+        verify &= (aut <<= spec);
+        BOOST_CHECK_MESSAGE(verify == expected, circuit + ": expected " + (expected ? "[OK]" : "[failed]"));
+    }
+}
+
 
 static void grover_oracle(AUTOQ::ConcreteAutomata& aut, unsigned ans, int n) {
     for (int i=1; i<=n; i++) {
diff --git a/unit_tests/testcase/MeasurePermutation/if_reset.qasm b/unit_tests/testcase/MeasurePermutation/if_reset.qasm
new file mode 100644
index 000000000..5f7132706
--- /dev/null
+++ b/unit_tests/testcase/MeasurePermutation/if_reset.qasm
@@ -0,0 +1,8 @@
+OPENQASM 3;
+include "stdgates.inc";
+qubit[3] q;
+bit r;
+r = measure q[1];
+if (r) {
+    x q[1];
+}
diff --git a/unit_tests/testcase/MeasurePermutation/if_wrong_qubit.qasm b/unit_tests/testcase/MeasurePermutation/if_wrong_qubit.qasm
new file mode 100644
index 000000000..39e1bc676
--- /dev/null
+++ b/unit_tests/testcase/MeasurePermutation/if_wrong_qubit.qasm
@@ -0,0 +1,8 @@
+OPENQASM 3;
+include "stdgates.inc";
+qubit[3] q;
+bit r;
+r = measure q[2];
+if (r) {
+    x q[1];
+}
diff --git a/unit_tests/testcase/MeasurePermutation/inv.hsl b/unit_tests/testcase/MeasurePermutation/inv.hsl
new file mode 100644
index 000000000..236ad7770
--- /dev/null
+++ b/unit_tests/testcase/MeasurePermutation/inv.hsl
@@ -0,0 +1,2 @@
+Extended Dirac
+{|sts> : |s|=1, |t|=1}
diff --git a/unit_tests/testcase/MeasurePermutation/post.hsl b/unit_tests/testcase/MeasurePermutation/post.hsl
new file mode 100644
index 000000000..556f46cde
--- /dev/null
+++ b/unit_tests/testcase/MeasurePermutation/post.hsl
@@ -0,0 +1,2 @@
+Extended Dirac
+{|s0s> : |s|=1}
diff --git a/unit_tests/testcase/MeasurePermutation/pre.hsl b/unit_tests/testcase/MeasurePermutation/pre.hsl
new file mode 100644
index 000000000..236ad7770
--- /dev/null
+++ b/unit_tests/testcase/MeasurePermutation/pre.hsl
@@ -0,0 +1,2 @@
+Extended Dirac
+{|sts> : |s|=1, |t|=1}
diff --git a/unit_tests/testcase/MeasurePermutation/while_reset.qasm b/unit_tests/testcase/MeasurePermutation/while_reset.qasm
new file mode 100644
index 000000000..08ac01674
--- /dev/null
+++ b/unit_tests/testcase/MeasurePermutation/while_reset.qasm
@@ -0,0 +1,9 @@
+OPENQASM 3;
+include "stdgates.inc";
+qubit[3] q;
+bit r;
+r = measure q[1];
+while (r) { // inv.hsl
+    x q[1];
+    r = measure q[1];
+}