Prolonged exposure to wood smoke as cooking fuel on a daily basis has been associated with increased occurrence of respiratory and other ailments. Accumulated data from developing countries have linked acute and chronic eye and respiratory conditions to indoor air pollution exposures. The present study compared self-reported eye and respiratory symptoms among women who used wood as fuel to those who used natural gas (NG) in a semi-rural setting from southern Pakistan. During the winter season, a total of 122 wood (n = 57) and NG users (n = 65) were interviewed regarding history of acute eye and respiratory symptoms the immediate past two weeks. In addition, histories of difficulty in breathing during the past year and of ever having asthma were also ascertained. Unadjusted estimates showed that wood users reported a higher frequency than NG users of eye congestion (odds ratio (OR) = 4.2, 95% confidence interval (CI) = 1.8-10.1), nasal congestion (OR = 2.5, 95% CI = 1.1-5.5), throat-related symptoms (OR = 5.4, 95% CI = 2.4-12.5), and cough (OR = 3.8, 95% CI = 1.7-8.6). Similarly, wood users had higher odds of reporting difficulty in breathing any time during the past year (OR = 3.9, 95% CI = 1.7-8.8) and ever having asthma (OR = 3.3, 95% CI = 1.5-8.1) compared to NG users. Our study showed an interactive effect of age with wood use. Acute eye symptoms were more frequently reported by wood users who were younger than age 28 years (OR = 5.1, 95% CI = 1.3-19.8) than by NG users; however, a smaller, marginally significant difference was observed in older women. A greater proportion of older wood users reported chronic respiratory symptoms, mainly cough (OR = 6.6, 95% CI = 1.9-26.7) than NG users, but no significant difference was observed for younger women. Throat-related symptoms were associated with wood use after adjusting for the effect of body mass index (BMI) (OR = 5.9, 95% CI = 2.6-14.2); eye and other respiratory symptoms were significantly associated with wood use only in women with a BMI of < 19.8 kg/m2. This cross-sectional study demonstrated that overall eye and respiratory symptoms were significantly associated with wood use in this setting. Future longitudinal study is needed to establish the etiological role of wood smoke in eye and respiratory ailments.