An ecological study was performed to identify patterns in the spatial distribution of neonatal mortality and risk areas as well as associated factors in Salvador, Bahia State, Brazil, 2000-2006. A thematic map was constructed, and techniques were used for formal assessment of spatial dependence. No spatial and spatial regression models were used to assess possible relationships between selected factors and spatial distribution of neonatal mortality. Spatial autocorrelation was observed in neonatal mortality (I = 0.17; p = 0.0100), so its distribution was non-random. The analysis showed a spatial pattern in which the highest risk (> 9.0/1,000 live births) was concentrated in the downtown areas and peripheral neighborhoods with the highest concentration of low-income families, and this was associated with the target risk factors. The proportion of low birth weight newborns was the only variable that was significantly associated with neonatal mortality. Living conditions may have contributed to the uneven spatial distribution of neonatal mortality in this city.