The use of internal combustion engines has so deeply penetrated into our life-style system that it is practically impossible to replace this versatile prime mover. However, the problem of fast depletion of conventional petroleum fuels have, of late, necessitated the search for alternative engine fuels. Besides, in the present day context, a major criterion of judicious selection of an alternative fuel is also based upon its low-emission characteristics. Hydrogen is the cleanest known alternative engine fuel. This paper discusses the nature and formation mechanism of different types of pollutants emitted from a hydrogen operated engine system. The concentration level of various pollutants emitted from both the spark ignition and compression ignition engine system configurations has been described. Practical engine operating conditions to bring down the pollutants to acceptable limits have also been identified.