Work-related musculoskeletal symptoms (WMSS) are one of the most common health problems around the world. These symptoms include discomfort such as pain, numbness, tingling, aching and stiffness felt on the different parts of the body. Body discomfort has been commonly associated with physically demanding working conditions, one of which is the small scale gold mining. However, there is little information about the association of body discomfort in the small scale gold mining and extraction in the Philippines to individual risk factors such as age, estimated height, years of work experience, alcohol consumption, and tobacco consumption of the workers. Thus, to provide a baseline data of the prevalence of body discomfort and its association to individual risk factors, a survey of 124 small scale gold mining and extraction workers in seven different mining sites from the north and south of the Philippines was conducted. The body discomfort questionnaire used is a 5-point scale rating on the frequency and severity of symptoms perceived in different parts of the body such a neck, shoulders, upper back, lower back, arms, elbows, hands or wrist, hips, thighs, knees, legs, and feet or ankle. Ninety five percent (95%) of the interviewees perceived body discomfort in at least one part of their bodies. Discomfort of body part found in the upper body, middle body, and extremities were found to be correlated; lower back (65.32%), shoulders (59.68%), and neck (54.03%) have the highest percentage. Spearman correlation was used to check for correlations between the frequency and severity of body discomfort and the individual factors. Results showed that severity of lower back discomfort and estimated alcohol consumption per week has low positive correlation (0.347). Frequency (0.315) and severity (0.305) of knee discomfort also have a low positive correlation to years of experience in mining. Binary logistic regression was used to obtain the significant risk factors that affect the presence of body discomfort. No individual factors were found to be significantly associated with presence of neck, upper back, shoulder, arms, hands/wrists, hips, thigh, legs, and feet/ ankle discomfort. Estimated alcohol consumption per week was found to be significantly associated with presence of discomfort on the lower back, years of experience in mining to presence of discomfort on the elbows, years of experience in mining and estimated height to presence of discomfort on the knees. In order to reduce, at most prevent, body discomfort, result of the study suggests that emphasis is needed on alcohol consumption, height of the tunnels and facilities, and work design of the mining and extraction processes. Further analysis of other possible risk factors is needed for the body discomfort with no association to the individual risk factors..