The objective of this study was to investigate the parents' attitudes towards and identify the possible factors associated with pandemic H1N1 vaccine uptake that was recommended to children between 6 months and 5 years of age. A questionnaire exploring the attitudes of parents to H1N1 vaccine was given to parents of children 6 through 60 months of age attending to Akdeniz and Gazi University Hospitals' well-child departments between 15 November 2009 and 15 January 2010. The questionnaire included questions on demographic characteristics, parental perception of the severity of the pandemic, the presence of anyone in their environment who suffered from pandemic influenza, their decision on whether or not to vaccinate their child, the factors that influenced them during decision-making process and possible factors that might have influenced the opponents of their decision. Those who accepted to get their children vaccinated got it immediately, free of charge. Out of 611 parents who responded the questionnaire 226 (36.7%) had their children vaccinated. Parental education period of less than 12 years, not being a close relative of a health care worker, not having a relative who suffered from the disease, having a child younger than 36 months, being influenced by the relatives' opinions or from the politicians or from the media all decreased vaccine acceptance. Factors that were most significantly associated with vaccine refusal were thinking that the pandemic was exaggerated (OR 9.44, 95% CI 4.28-20.82) and believing that other preventive measures were more effective than H1N1 vaccine (OR 15.61, 95% CI 7.37-33.08). Lessons learned from influenza H1N1/2009 pandemic may help national authorities, health care providers and media on how to keep the public well informed and find ways of better risk-benefit communication with the parents on vaccines.