The Mars Orbiter Laser Altimeter (MOLA) instrument operated as an atmospheric lidar system as well as an altimeter, detecting absorptive clouds in northern latitudes shortly after orbit insertion in October 1997 and reflective clouds over the north polar cap at the start of the Science Phasing Orbits in March 1998. Global cloud measurements commenced with the primary mapping mission in March 1999, with nearly continuous coverage for 1.25 Mars years. MOLA tracked several dust storms, culminating with a major dust storm in June 2001. Reflective clouds, exhibiting distinctive patterns governed by insolation and the dynamics of the atmosphere, were detected at elevations up to 20 km above the surface, chiefly in the polar winter night. MOLA distinguishes cloud returns by pulse width and energy measurements. Unusually strong and brief reflections with minimal extinction suggest precipitation of CO2 snow under supercooled conditions. Weaker cloud reflections occurred at all latitudes. Some reflective daylight clouds at low latitudes suggested convective vortices or dust devils. Ground fogs composed of dust and H2O ice formed at night along the seasonal frost line. Absorptive clouds, while not resolved altimetrically, tracked the advancing and receding edges of the seasonal polar caps. The absorptive and reflective clouds provide a seasonal profile of atmospheric activity spanning two Martian years. Winter reflective cloud activity declined to background levels earlier in the second year at both poles, suggesting interannual warming.