paper presents an analytical study of magnetohydrodynamics and convective heat transfer of nanofluids synthesized by three different shaped (brick, platelet and cylinder) silver (Ag) nanoparticles in water. A two-phase nanoscale formulation is adopted which is more appropriate for biophysical systems. The flow is induced by metachronal beating of cilia and the flow geometry is considered as a cylindrical tube. The analysis is carried out under the low Reynolds number and long wavelength approximations and the fluid and cilia dynamics is of the creeping type. A Lorentzian magnetic body force model is employed and magnetic induction effects are neglected. Solutions to the transformed boundary value problem are obtained via numerical integration. The influence of cilia length parameter, Hartmann (magnetic) number, heat absorption parameter, Grashof number (free convection), solid nanoparticle volume fraction, and cilia eccentricity parameter on the flow and heat transfer characteristics (including effective thermal conductivity of the nanofluid) are examined in detail. Furthermore a comparative study for different nanoparticle geometries (i.e. bricks, platelets and cylinders) is conducted. The computations show that pressure increases with enhancing the heat absorption, buoyancy force (i.e. Grashof number) and nanoparticle fraction however it reduces with increasing the magnetic field. The computations also reveal that pressure enhancement is a maximum for the platelet nano-particle case compared with the brick and cylinder nanoparticle cases. Furthermore the quantity of trapped streamlines for cylinder type nanoparticles exceeds substantially that computed for brick and platelet nanoparticles, whereas the bolus magnitude (trapped zone) for brick nanoparticles is demonstrably greater than that obtained for cylinder and platelet nanoparticles. The present model is applicable in biological and biomimetic transport phenomena exploiting magnetic nanofluids and ciliated inner tube surfaces. (C) 2016 The Society of Powder Technology Japan. Published by Elsevier B.V. and The Society of Powder Technology Japan. All rights reserved.