- KLR650-A: The "A" model was introduced in 1987, based on its KLR600 predecessor (1984-1986). The "A" model remained nearly unchanged until the introduction of the 2008 model in USA, Canada and Europe
- KLR650-B or Tengai: was sold in the USA starting 1990 and in other countries for several years afterward
- KLR650-C: The "C" model is a more dirt-oriented motorcycle fitted with stiffer 41mm front forks, improved brakes, tubular engine guard, smaller 14 liter fuel tank, and steel wheel rims. Lacking a temperature gauge, it has an over-heat lamp.
- KLR650-E: 2008 was the first major redesign of the KLR650. The primary changes include upgraded 41mm forks, a new D-section swingarm, dual beam headlight, dual-piston rear brake caliper, upgraded cooling system, 4mm spokes, cowling and fairing redesign as well as various redesigned parts. (error corrected specifications)
- The U.S. Military have KLR650s modified by Hayes Diversified Technologies to burn military-spec fuels including diesel. All-new engines were designed to replace the 4-stroke gasoline engines. See HDT KLR650s
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