Delayed onset muscle soreness

Although the precise cause is still unknown, the type of muscle contraction seems to be a key factor in the development of DOMS. Exercises that involve many eccentric contractions, such as downhill running, will result in the most severe DOMS. This has been shown to be the result of more muscle cell damage than is seen with typical concentric contractions, in which a muscle successfully shortens during contraction against a load.^[2]

Some research^[3] claims that DOMS is not caused by the pain from damaged muscle cells, but from the reinforcement process. The muscle responds to training by reinforcing itself up to and above its previous strength by adding new sarcomeres—the segments in the muscle fibrils. This reinforcement process causes the cells to swell and put pressure on nerves and arteries, causing DOMS.

Wikipedia: DOMS