Background: The literature on complementary and alternative (CAM) therapies in South East Asia is limited. The objective of the study was to evaluate the frequencies of CAM therapies in the Malaysian patients with migraine and tension-type headache (TTH). We also assessed the reasons for CAM use. Methods: This was a cross-sectional study. The study was conducted in a tertiary hospital in Malaysia. Consecutive patients presenting with migraine and TTH to the neurology clinic were recruited. Demographic characteristics were documented. Data on CAM use, including frequency and the reasons was collected. Results: Six hundred and eighty five patients (365 TTH and 320 migraine) were recruited. They consisted of 305 (44.5%) Malay, 174 (25.4%) Chinese, 169 (24.7%) Indian and 37 (5.4%) patients from other ethnic groups. A total of 478 (69.8%) patients, comprising 266 (55.6%) patients with TTH and 212 (44.4%) patients with migraine used CAM therapies. The most commonly used CAM therapies were medicated oil (355 patients, 51.8%) and massage (246 patients, 35.9%). The most common reasons for CAM use were reduction of pain (47.7 %), stress reduction (34.9%), and “cooling” effect (27.4%). Thirteen (4.1%) patients with migraine practiced reflexology, whereas 5 (1.4%) patients with TTH practiced reflexology (p=0.032). Twenty three (7.2%) patients with migraine took vitamin supplements compared to 13 (3.6%) patients with TTH (p=0.039). On univariate analysis, CAM use was significantly associated with ethnic groups (p=0.014), gender (p<0.0001), age (p=0.004), salary (p=0.014), educational level (p=0.003), and headache subtypes (p= 0.067). On logistic regression, married women were more likely to use CAM (OR=1.864, 95% CI 1.216-2.858, p=0.004). Conclusion: A large number of Malaysian headache patients used CAM. The most common reasons were reduction of pain, stress and “heatiness”. Medicated oil was most commonly used, followed by massage. Married women were more likely to use CAM, and this was the only determinant in this study.