Incidence rates of childhood leukemia vary between different regions of the world. The objective of this study was to test possible trends in incidence rate of early childhood leukemia (children <5 years old at the diagnosis) in Brazil. Data from 18 population-based cancer registries (PBCRs) were analyzed (period 1999-2010). The analysis consisted of frequencies, age-adjusted incidence rates, and joinpoint regression results, including annual average percent change (AAPC) in incidence rates and 95% confidence intervals (CIs). The median age-adjusted incidence rate (AAIR) of overall early childhood leukemia was 61 per million. The AAIR for acute lymphoid leukemia (ALL) was 44 per million and nonlymphoid acute leukemia (NLAL) was 14 per million. The median ALL/NLAL ratio was 3.0, suggesting higher incidence rate of NLAL in these settings. The joinpoint analysis demonstrated increased leukemia incidence rate in João Pessoa (AAPC = 20; 95% CI: 3.5, 39.4) and Salvador (AAPC = 8.68; 95% CI: 1.0, 16.9), respectively, whereas incidence rate in São Paulo PBCR decreased (AAPC = -4.02%; 95% CI: -6.1%, -1.9%). Correlation between ALL AAIR and selected variables of socioeconomic (SES) factors was not observed. Increased AAIR regionally overtime was observed. However, the interpretation for such phenomenon should be cautious because it might reflect the access to health care, diagnosis procedures, and improvement of PBCR´s quality. The observed trend supports the necessity of further ecological studies.