A recent expedition to the equatorial Pacific surveyed over 60,000 km2 of seafloor using swath map imaging and high-resolution seismic profiling. This survey revealed the common occurrence of large pits in the biogenic sediments that are usually associated with basement highs. The pits range in size up to a few kilometers across and are on the order of 50 m -- 100 m deep. They were found on seafloor ranging in age from 15 Ma to 55 Ma, with overlying sediment cover up to 500 m thick. We link their origin with hydrothermal discharge through conduits created by differential compaction and fracturing over basement highs and by basement faulting that penetrates the overlying sediments. Although carbonate dissolution is likely to be associated with the formation of the pits, their occurrence shows no consistent relationship with the present calcite compensation depth (CCD).