The significant reduction of bollworm infestation by the implementation of Integrated Pest Management (IPM) in Bt Cotton as a component of IPM led to reduction in bollworm infestation and increase in yield. However, these alterations have brought in many new biotic problems hitherto unknown or of little economic importance. Field survey of rainfed Bt cotton fields in Perambalur district of Tamil Nadu, India during 2008-2014 revealed that the incidence of various insect pests and plant diseases is on the rise in different Bt cotton hybrids. In 2008-2009, it was observed that the Bt cotton was damaged by cotton mealybug (Phenacoccus solenopsis Tinsley), green mirid bug (Creontiades biseratance Distant) and root rot (Rhizoctonia solani Kuhn) which caused severe yield losses. In addition to that, other pests like papaya mealybug (Paracoccus marginatus Williams & Granara de Willink) and Alternaria leaf spot caused more damage in Bt cotton during 2009-10. Besides these pests, the mirid bug (Campyloma livida Reuter), stripped mealybug (Ferrissia virgata Ckll), tobacco streak virus, grey mildew Ramularia areola and boll rot incidence in Bt cotton were noticed in 2010-12. Apart from this pest and disease problems, the Alterrnaria leaf blight, root rot (Macrophomina phaseolina Maubl) and Myrothecium leaf spot caused severe yield losses in Bt cotton during 2012-2014. The survey revealed that, the pests and disease problems are increasing year by year in Bt cotton which caused yield reduction and also increased the cost of cultivation. If left unchecked these pests and disease problems are capable of undoing all benefits gained due to Bt cotton in terms of increased yield and reduction in use of chemical pesticides.