One of the most promising solutions to address the twin problems of transport related pollution and energy security is to use alternative fuels. Compressed Natural gas (CNG) has been widely used in India to address the menace of pollution from commercial vehicles in cities like Delhi. Hydrogen blended compressed natural gas (HCNG) as a fuel has potential for further reducing harmful emissions and greenhouse gases. Enriching hydrogen in CNG improves combustion characteristic of CNG and reduces carbonyl emissions. Due to growing concerns over un-regulated emissions and their effect on human health, it is imperative to estimate un-regulated emissions from such alternatives for assessing overall impact of such fuels.Presently world over, emission legislations mainly addresses pollutants like CO, HC, NOx, CH4, NH3, PM etc. Relatively higher quantity in exhaust qualifies these pollutants to be monitored and controlled. But as the consumption of alternative fuels becomes comparable to that of the liquid fuels, other unregulated emissions like Methanol (CH3OH), Ethanol (C2H5OH), Formaldehyde (HCHO), Acetaldehyde (CH3CHO), Formic Acid (HCOOH), Acetic Acid (CH3COOH), Propene (C3H8), Ethylene (C2H4), Ethyne (C2H2) Benzene (C6H6), 1,3-Butadiene (1,3-C4H6), Toluene (C7H8), Butene (C4H8) etc. become significant.This paper presents the study of unregulated emissions on a heavy duty six cylinder engine used in the transport buses with CNG and HCNG as fuels. A transient engine dynamometer set up was used along with Fourier Transform Infrared Spectroscopy Gas Analyzer (FTIR) for measuring unregulated emissions. It was observed from the test results that regulated emissions like CO, NO, HC and PM are considerably reduced with HCNG fuel. Also, unregulated emissions like Formic Acid (HCOOH), Propane (C3H8), Ethylene (C2H4), Ethyne (C2H2), Benzene (C6H6), 1,3-Butadiene (1,3-C4H6), Toluene (C7H8) and Butene (C4H8) are significantly reduced with HCNG fuel. Whereas, there is slight increase in Methanol (CH3OH), Ethanol (C2H5OH), Formaldehyde (HCHO) and Acetaldehyde (CH3CHO) with HCNG.It can be inferred from the study that HCNG has reduced significant amount of unregulated emissions and it is the most promising fuel for transport sector in future. Beside this it is also observed that with HCNG Fuel, there is increase in NH3 and NO2 which create favorable condition for effective working of exhaust after treatment device like selective catalytic reduction (SCR) for Euro VI compliant vehicles.