This study aims to examine the effect of socioeconomic status (hereafter, SES) on healthcare utilization of the patients with rare and incurable diseases. Information of 2,973 patients who were self-employed insured and utilized healthcare service in 2007 was drawn from the National Health Insurance (hereafter, NHI) claim data. SES was set as four groups based on the monthly contribution. Outcome variable was the expense for outpatient and in-hospital services, which was log-transformed and square-rooted in oder to obtain normal distribution. Covariates included age, gender, residence and diagnosis. To examine the effects after controlling for covariates, we employed generalized estimating equation model, since patients with the same diagnosis are likely to have similar characteristics of demographics and healthcare utilization. Univariate statistics showed that lower SES was associated with less utilization of healthcare services. After controlling for covariates, a significantly smaller amount of money was expended for the lowest SES group compared to the highest one. Rural residence was associated with less utilization, except that residents in Seoul significantly more utilized outpatient services in tertiary hospitals. Considering that there is a subsidy program for the low income patients, such differences in healthcare utilization according to SES seems to result from the burden of out-of-pocket payments for uncovered services of the NHI.