Background: How socio-demographic factors influence women's autonomy in decision making on health care including purchasing goods and visiting family and relatives are very poorly studied in Nepal. This study aims to explore the links between women's household position and their autonomy in decision making. Methods: We used Nepal Demographic Health Survey (NDHS) 2006, which provided data on ever married women aged 15-49 years (n = 8257). The data consists of women's four types of household decision making; own health care, making major household purchases, making purchase for daily household needs and visits to her family or relatives. A number of socio-demographic variables were used in multivariable logistic regression to examine the relationship of these variables to all four types of decision making. Results: Women's autonomy in decision making is positively associated with their age, employment and number of living children. Women from rural area and Terai region have less autonomy in decision making in all four types of outcome measure. There is a mixed variation in women's autonomy in the development region across all outcome measures. Western women are more likely to make decision in own health care (1.2-1.6), while they are less likely to purchase daily household needs (0.6-0.9). Women's increased education is positively associated with autonomy in own health care decision making (p < 0.01), however their more schooling (SLC and above) shows non-significance with other outcome measures. Interestingly, rich women are less likely to have autonomy to make decision in own healthcare. Conclusions: Women from rural area and Terai region needs specific empowerment programme to enable them to be more autonomous in the household decision making. Women's autonomy by education, wealth quintile and development region needs a further social science investigation to observe the variations within each stratum. A more comprehensive strategy can enable women to access community resources, to challenge traditional norms and to access economic resources. This will lead the women to be more autonomous in decision making in the due course.