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We studied the ecology of the Lesser Kestrel Falco naumanni, a globally threatened species, to identify the factors causing its gradual decline in Israel, in order to stabilize and possibly restore its numbers. Lesser Kestrels in Israel breed in colonies, both adjacent to human settlements (rural and urban) and in the countryside, where they are found especially on cliffs. In this study, observations of Lesser Kestrels were carried out in three different breeding areas: (1) an urban colony in Jerusalem, (2) a rural colony in the Alona district and (3) a cliff in the Judean desert (open landscape colony) about 10 km east of Jerusalem. The number of fledglings per nest in Jerusalem (1.91) was lower than in Alona (2.44) and the cliff (3.16). As this lower productivity was associated neither with the clutch size, with hatching success, which were similar in all three regions (about four eggs per clutch, and 80% hatched, respectively), nor with egg fertility, it probably reflects factors operating during the nestling phase. We suggest that the two main factors limiting food availability and causing nestling deaths in Jerusalem are the relatively long flight distances between the breeding and hunting sites, and the use of pesticides in the city parks and lawns. Stochastic events superimposed on such factors, such as the drought of 1999, which markedly reduced productivity, may cause pronounced fluctuations eventually affecting long-term population persistence.