diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index ea47cfebda80..47641c9c8038 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -32,6 +32,7 @@ Removed
 
 Fixed
 -----
+- Fix issue with skip_transpiler causing some gates to be ignored silently.
 
 
 `0.5.4`_ - 2018-06-11
diff --git a/qiskit/_compiler.py b/qiskit/_compiler.py
index 2b70d62c35f4..fa756d46f29e 100644
--- a/qiskit/_compiler.py
+++ b/qiskit/_compiler.py
@@ -126,9 +126,11 @@ def compile(circuits, backend,
         if skip_transpiler:  # Just return the qobj, without any transformation or analysis
             job["config"]["layout"] = None
             job["compiled_circuit_qasm"] = circuit.qasm()
+            basis_all = "id,u0,u1,u2,u3,x,y,z,h,s,sdg,t,tdg,rx,ry,rz," \
+                        "cx,cy,cz,ch,crz,cu1,cu3,swap,ccx,cswap"
             job["compiled_circuit"] = DagUnroller(
                 DAGCircuit.fromQuantumCircuit(circuit),
-                JsonBackend(job['config']['basis_gates'].split(','))).execute()
+                JsonBackend(basis_all.split(','))).execute()
         else:
             if initial_layout is None and not backend.configuration['simulator']:
                 # if coupling_map is not already satisfied, pick a good initial layout