We present an updated catalogue of 113 X-ray flares detected by Swift in the ∼33 per cent of the X-ray afterglows of gamma-ray burst (GRB). 43 flares have a measured redshift. For the first time the analysis is performed in four different X-ray energy bands, allowing us to constrain the evolution of the flare temporal properties with energy. We find that flares are narrower at higher energies: their width follows a power-law relation w∝E−0.5 reminiscent of the prompt emission. Flares are asymmetric structures, with a decay time which is twice the rise time on average. Both time-scales linearly evolve with time, giving rise to a constant rise-to-decay ratio: this implies that both time-scales are stretched by the same factor. As a consequence, the flare width linearly evolves with time to larger values: this is a key point that clearly distinguishes the flare from the GRB prompt emission. The flare 0.3–10 keV peak luminosity decreases with time, following a power-law behaviour with large scatter: Lpk∝t−2.7±0.5pk. When multiple flares are present, a global softening trend is established: each flare is on average softer than the previous one. The 0.3–10 keV isotropic energy distribution is a lognormal peaked at 1051 erg, with a possible excess at low energies. The flare average spectral energy distribution is found to be a power law with spectral energy index β∼ 1.1. These results confirmed that the flares are tightly linked to the prompt emission. However, after considering various models we conclude that no model is currently able to account for the entire set of observations.