Influenza vaccination is recommended for children with chronic medical conditions yet is infrequently performed. The reasons for low influenza vaccination rates in this group have not been well studied. We assessed and compared parents of children with chronic medical conditions regarding their beliefs and attitudes about influenza vaccination in 2003 and 2004. Parents of 2- to 13-year-old children with chronic medical conditions from health centers in low-income urban neighborhoods completed a 19-question survey, mailed following the 2002-2003 and 2003-2004 influenza seasons. Parent-reported influenza vaccination rate declined from 2003 (44%) to 2004 (25%). The most important factors related to influenza vaccination status were perceived doctor's recommendation (odds ratio [OR] = 6.0, 95% confidence interval [CI] = 3.7-9.7), parents' belief that the child should be vaccinated (OR = 5.4, 95%CI = 3.3-8.8), relatives' belief that the child should be vaccinated (OR = 1.7, 95%CI = 1.1-2.7), easy access to the doctor's office for a flu shot (OR = 2.4, 95%CI = 1.4-4.2), and receipt of a reminder from the doctor's office (OR = 1.7, 95%CI = 1.1-2.6). In 2004 compared with 2003, fewer parents reported getting a reminder, and fewer believed that their child's doctor recommended flu vaccine. Doctors' recommendation that children with chronic medical conditions should receive an annual influenza vaccine and vaccine availability are important factors that resulted in a higher likelihood of influenza vaccination. Our findings that fewer parents reported receiving reminders and that fewer children were vaccinated in 2004 suggest that sustained improvements in vaccination rates may require continual changes in the format and delivery method of vaccination reminders from physicians.