  Context. Recent observations of the X-ray emission from T Tauri stars in the
Orion nebula have shown that they undergo frequent outbursts in their X-ray
luminosity. These X-ray flares are characterised by increases in luminosity by
two orders of magnitude, a typical duration of less than one day, and a
significant hardening of the X-ray spectrum.
  Aims. It is unknown what effect these X-ray flares will have on the
ionisation fraction and dead-zone structure in protoplanetary disks. We present
the results of calculations designed to address this question.
  Methods. We have performed calculations of the ionisation fraction in a
standard $\alpha$-disk model using two different chemical reaction networks. We
include in our models ionisation due to X-rays from the central star, and
calculate the time-dependent ionisation fraction and dead--zone structure for
the inner 10 AU of a protoplanetary disk model.
  Results. We find that the disk response to X-ray flares depends on whether
the plasma temperature increases during flares and/or whether heavy metals
(such as magnesium) are present in the gas phase. Under favourable conditions
the outer disk dead--zone can disappear altogether,and the dead-zone located
between 0.5 < R < 2 AU can disappear and reappear in phase with the X-ray
luminosity.
  Conclusions. X-ray flares can have a significant effect on the dead-zone
structure in protoplanetary disks. Caution is required in interpreting this
result as the duration of X-ray bursts is considerably shorter than the growth
time of MHD turbulence due to the magnetorotational instability.
