The success of micropropagation depends on a number of factors, which affect directly or indirectly on proper establishment of explants in the medium. In Andrographis paniculata fungal contamination occurs within 3-4 days of inoculation when the explants were collected from the field grown mother bushes. Spraying of 1000ppm carbendazim, a day prior to the collection controls the fungal contamination. While bacterial contamination can be overcome by surface sterilizing the explant with bleaching powder, broad spectrum antibiotics like amoxycillin, 70% alcohol and the chemical sterilent mercuric chloride. Addition of 200mg/l amoxycillin in the media can reduce the bacterial contamination by 90-95%.