This article describes the recent progress of optical lattice clocks with neutral strontium ( 87 Sr), ytterbium ( 171 Yb) and mercury ( 199 Hg) atoms. In particular, we present frequency comparison between the clocks locally via an optical frequency comb and between two Sr clocks at remote sites using a phase-stabilized fibre link. We first review cryogenic Sr optical lattice clocks that reduce the room-temperature blackbody radiation shift by two orders of magnitude and serve as a reference in the following clock comparisons. Similar physical properties of Sr and Yb atoms, such as transition wavelengths and vapour pressure, have allowed our development of a compatible clock for both species. A cryogenic Yb clock is evaluated by referencing a Sr clock. We also report on a Hg clock, which shows one order of magnitude less sensitivity to blackbody radiation, while its large nuclear charge makes the clock sensitive to the variation of fine-structure constant. Connecting all three types of clocks by an optical frequency comb, the ratios of the clock frequencies are determined with uncertainties smaller than possible through absolute frequency measurements. Finally, we describe a synchronous frequency comparison between two Sr-based remote clocks over a distance of 15 km between RIKEN and the University of Tokyo, as a step towards relativistic geodesy.