We demonstrate fabrication of microchips with microfluidic structures for dynamic analysis of living cells using a femtosecond (fs) laser. Fs laser direct writing followed by annealing and successive wet etching in dilute hydrofluoric (HF) acid solution resulted in formation of three dimensional (3D) hollow microstructures embedded in photostructurable glass. The embedded microchannel structure enabled us to analyze unique phenomenon of Cryptomonas, which suddenly swims very fast under certain condition. Vector analysis of the driving force for the rapid motion was also carried out by introducing nano-beads into the microchannel, in which Cryptomonas was encapsulated. We also fabricated a microchip for observation of Phormidium moving toward a seedling root, which accelerates growth of the seedling. Using the embedded microchannel in the microchip, observation of Phormidium assemblage to the seedling root was easily carried out. Such microchips with microfluidic structures, referred to as a nano-aquarium, realize the efficient and highly functional observation of living cells. (C) 2009 Elsevier B.V. All rights reserved.