We analysed data collected on board commercial purse seine vessels in the Aegean and Ionian Seas (eastern Mediterranean Sea, Greece) in 13 seasonal sampling periods from 2003 to 2008 in order to describe the composition of the retained and discarded catch and shed light on discarding practices. In each area, five species constituted the majority of the marketable catch (>97%): sardine (Sardina pilchardus), anchovy (Engraulis encrasicolus), round sardinella (Sardinella aurita), bogue (Boops boops) (in both areas), mackerel (Scomber japonicus; in the Aegean Sea) and picarel (Spicara smaris; in the Ionian Sea). Discarded quantities were on average 4.6% and 2.2% of the total catch in terms of weight in the Aegean and Ionian Seas respectively. Discards on the marketable ratio fluctuated over years and seasons without showing any particular trend. At the species level, sardine and mackerel were seldom discarded while large amounts of anchovy were discarded only during its recruitment period (autumn), when juvenile fish dominate the population. The discarding ratio for bogue, picarel and round sardinella ranged from zero to total discarding because they constitute a supplementary source of income for the fishers. Discarded fish comprised mainly small individuals for all species considered with the exception of round sardinella. However, the lengths at which 50% of the individuals were discarded were generally small, often smaller than the species minimum landing sizes. Geographical coordinates and marketable catch explained part of the variability of the discarded quantities, as revealed by generalized additive models. Discarding practices and implications for management of purse seine fisheries are also discussed.