A diethylcarbamazine (DEC)-fortified salt intervention programme was implemented between 1982 and 1986 in Karaikal district, Union territory of Pondicherry, south India, to control Culex transmitted bancroftian filariasis. The intervention reduced the microfilaria (Mf) rate from 4.49% to 0.08%. To eliminate the residual microfilaraemia, the health department detected and treated Mf carriers from 1987 to 2005 and mass-administered drugs in 2004 and 2005. Surveillance from 1987 to 2005 revealed persistent microfilaraemia in 0.03-0.42% of the population. In 2006, we conducted a more detailed Mf survey and a child antigenaemia (Ag) survey in 15 urban wards and 17 rural villages. These surveys showed an overall Mf rate of 0.46% in the high-risk urban areas and 0.18% in the rural areas; none of the sampled children was positive for Ag. All detected Mf carriers were >20 years old. The age of the youngest Mf carrier was 30 years in urban and 21 years in rural areas, which suggests that transmission was interrupted and there was no incidence of new Mf case after cessation of DEC salt programme. Eleven of 15 urban and 15 of 17 villages were totally free from microfilaraemia. Nevertheless, three of 15 surveyed urban localities and two of 17 villages showed >1% Mf rate. Thus, it seems that (i) post-intervention very low levels of microfilaraemia can continue as long as 20 years; (ii) 0.60-0.70% Mf rate is a safe level and at this level recrudescence of infection may not occur; (iii) there can be isolated localities with >1% Mf rate and their detection for further intervention measures could be challenging in larger control/elimination programmes and (iv) the residual infection mostly gets concentrated in the adult population, in underdeveloped urban areas and in historically highly endemic or large endemic rural areas. These groups and areas should be targeted with rigorous intervention measures such as mass drug administration to eliminate the residual infection.