BACKGROUND: Otitis media (OM) morbidity in American Indian and Alaska Native (AI/AN) children is historically higher than that in other US children. METHODS: Outpatient visits and hospitalizations listing OM as a diagnosis and outpatient visits listing myringotomy with insertion of tubes as a procedure among AI/AN children <5 years of age from the Indian Health Service National Patient Information Reporting system for 2003-2005 were analyzed. Outpatient visits and hospitalizations with OM for the general US child population were analyzed using the National Hospital Ambulatory Medical Care and National Ambulatory Medical Care Surveys for 2003-2005, and the 2003 Kids' Inpatient Database, respectively. RESULTS: The OM-associated outpatient visit rate for AI/AN children <5 years of age (89 per 100 children/yr) for 2003-2005 was less than that reported for 1994-1996 (138); however, the rate increased for Alaska region (158 to 181). The OM outpatient visit and myringotomy with insertion of tubes rates (181 and 2.6 per 100 children/yr, respectively) for AI/AN children in Alaska were higher than rates for children in each of the other IHS regions and rates for US children (63 and 1.8 per 100 children/yr, respectively). The OM outpatient visit rates for AI/AN infants (184), especially in the Alaska region (334), were higher than the rate for US infants (84). CONCLUSIONS: The OM-associated outpatient visit rate in AI/AN children <5 years of age has decreased but remains higher than that of the US general child population; however, the rate increased in the Alaska region, where a limited decline in invasive pneumococcal disease has been demonstrated. The ongoing disparity in OM outpatient visit rates among AI/AN children, especially Alaska Native children, indicates a need for new prevention measures, including expanded-valency pneumococcal conjugate vaccines, to reduce OM morbidity.