As the fossil fuels are depleting day by day due to heavy demand in various sectors like agriculture, transport etc., escalation of fuel prices in International Oil Market causing economic burden on developing countries like India and increase of environmental problems like Global warming and Green-house effect with IC engine with the use of fossil fuels, the search for alternative fuels has become pertinent and necessary. Gaseous fuels have many advantages than liquid fuels, as their calorific values of fuels are high, pollutants emitted by gaseous fuels are low and less dangerous when compared with liquid fuels. The drawbacks associated with use of vegetable oils in diesel engines such as high viscosity and low volatility can be reduced to some extent by converting them into biodiesel. However, they (biodiesel) cause combustion problems in diesel engine and hence call for low heat rejection (LHR) engine, which can burn low calorific value fuel, give high heat release rate and faster rate of combustion. They are many methods to induct gaseous fuels such as port injection, carburetion technique, injection of gaseous fuel at the near end of compression stroke etc,. Investigations were carried out with biogas gas as primary fuel inducted by port injection and cottonseed biodiesel was injected into the engine in conventional manner. Particulate matter (PM), oxides of nitrogen (NOx), carbon mono oxide (CO) levels and un-burnt hydro carbons (UBHC) are the exhaust emissions from a diesel engine. They cause health hazards, once they are inhaled in. They also cause environmental effects like Green-house effect and Global Warming. Hence control of these emissions is an immediate effect and an urgent step. The pollutants of PM, NOx,CO and UBHC were