System-architecture　design　optimization　of　flow-based　microfluidic　biochips　has　been　extensively　investigated　over　the　past　decade.　Most　of　the　prior　work,　however,　is　still　based　on　chip　architectures　with　dedicated　storage　units　and　this,　not　only　limits　the　performance　of　biochips,　but　also　increases　their　fabrication　cost.　To　overcome　this　limitation,　a　distributed　channel-storage　architecture　can　be　implemented,　where　fluid　samples　can　be　cached　temporarily　in　flow　channels　instead　of　using　a　dedicated　storage.　This　new　concept　of　fluid　storage,　however,　requires　a　careful　arrangement　of　fluid　samples　to　enable　the　channels　to　fulfill　the　dual　functions　of　transportation　and　caching.　Moreover,　to　avoid　cross-contamination　between　different　fluidic　flows,　wash　operations　are　necessary　to　remove　the　residue　left　in　flow　channels.　In　this　article,　we　formulate　the　first　practical　system　level　design　and　wash　optimization　problem　for　microfluidic　biochips　with　distributed　channel　storage　architecture,　considering　high-level　synthesis,　physical　design,　and　wash　optimization　simultaneously,　and　present　a　top-down　design　flow　to　solve　this　problem　systematically.　Given　the　protocol　of　a　biochemical　application　and　the　corresponding　design　requirements,　our　goal　is　to　generate　a　chip　architecture　with　low　fabrication　cost.　Meanwhile　the　biochemical　application　can　be　executed　efficiently　with　an　optimized　wash　scheme.　Experimental　results　on　multiple　benchmarks　confirm　that　our　approach　leads　to　short　completion　time　of　biochemical　applications,　low　chip　cost,　as　well　as　high　wash　efficiency.