Recent　advances　in　continuous-flow　microfluidics　have　enabled　highly　integrated　lab-on-a-chip　biochips.　These　chips　can　execute　complex　biochemical　applications　precisely　and　efficiently　within　a　tiny　area,　but　they　require　a　large　number　of　control　ports　and　the　corresponding　control　logic　to　generate　required　pressure　patterns　for　flow　control,　which,　consequently,　offset　their　advantages　and　prevent　their　wide　adoption.　In　this　article,　we　propose　the　first　flow-control　layer　co-synthesis　flow　called　MiniControl,　for　continuous-flow　microfluidic　biochips　under　strict　constraints　for　control　ports,　incorporating　high-level　synthesis,　physical　design,　and　control　system　design　simultaneously,　which　has　never　been　considered　in　previous　work.　With　the　maximum　number　of　allowed　control　ports　specified　in　advance,　this　synthesis　flow　aims　to　generate　biochip　architectures　with　high　execution　efficiency　and　the　corresponding　control　systems　with　optimized　timing　performance.　Besides,　the　overall　cost　of　a　biochip　can　be　reduced　and　the　tradeoff　between　a　control　system　and　execution　efficiency　of　biochemical　applications　can　be　evaluated　for　the　first　time.　The　experimental　results　demonstrate　that　MiniControl　leads　to　high　execution　efficiency,　low　platform　cost,　as　well　as　excellent　timing　performance,　while　strictly　satisfying　the　given　control-port　constraints.　©　1982-2012　IEEE.