Implementation of the General System of Social Security in Health (GSSSH) was initiated for the control of tuberculosis (TBC) in the state of Valle del Cauca, Colombia, between 1991-2000. A study of its effects was centered in 7 municipalities of Valle del Cauca with a complementary set of qualitative and quantitative techniques for data collection and analysis. A reduction in planning, control and regulation of TBC activities by state agencies was observed. New administrative structures and new funding sources did not produce the expected positive effects on tuberculosis control. Instead, the quantity and quality of tuberculosis control activity were reduced as a consequence of the health sector reform. In conclusion, GSSSH implementation affected negatively tuberculosis control activity.