The study explored socio-economic and geographic inequalities that exist in healthcare seeking, expenditures and methods of paying for healthcare. The study was conducted in two communities (one rural and urban) in Southeast Nigeria. A pre-tested questionnaire was administered to household heads or their representatives by trained interviewers. A socio-economic status (SES) index, together with urban-rural comparisons was used to examine the inequalities. The expenditures on healthcare and the proportions of respondents that used the different payment strategies were compared across SES quartiles and between the urban and rural areas. There were varying degrees of socio-economic and geographic inequalities in treatment expenditures, providers seen and payment modalities that were used. User fee without reimbursement was the commonest type of payment strategy, followed distantly by instalment payment. The two poorest quartiles were less likely to have used user fee and they mostly used instalment payment in the rural area. Logistic regression analysis showed that location was significantly and positively related to user fee but not to instalment payment. In conclusion, the poorest SES group and rural dwellers are the major sufferers of inequality and this could be mitigated through improved provision of primary healthcare services in rural areas and initiation of exemptions, vouchers and other pro-poor payment strategies for the poorest SES groups.