What causes your muscles to burn after a workout?

Lactic acid accumulation has been assumed to be the cause of muscle burn for many years. In the past few years, it has been discovered that lactic acid is not a by-product but is actually a source of fuel for muscles. So very little accumulates in the cells and greater lactic acid presence helps endurance, by providing needed fuel. Lactic acid will disappear within an hour of exercising, and is no longer thought to be responsible for muscle soreness that may appear 1-3 days after exercising.

Current thinking holds that calcium is the primary culprit for muscle soreness. Muscles contract through neuronal activation of calcium channels, which in turn cause the activation of contractile proteins. However, after continued activation, calcium channels become leaky. The muscles fatigue due to running out of the calcium supply to keep them contracting. As for the burn itself, it is not entirely clear. Some researchers hold that the same leaky calcium channels are also responsible for muscle burn, but it may just as well be other substrates within the muscle cells that are responsible.