Transgenic Huntington's disease (HD) mice, expressing exon 1 of the human HD gene (lines R6/1 and R6/2), are totally resistant to striatal lesions caused by the NMDA receptor agonist quinolinic acid (QA). Here we show that this resistance develops gradually over time in both R6/1 and R6/2 mice, and that it occurred earlier in R6/2 (CAG‐155) than in R6/1 (CAG‐115) mice. The development of the resistance coincided with the appearance of nuclear inclusions and with the onset of motor deficits. In the HD mice, hippocampal neurons were also resistant to QA, especially in the CA1 region. Importantly, there was no change in susceptibility to QA in transgenic mice with a normal CAG repeat (CAG‐18). R6/1 mice were also resistant to NMDA‐, but not to AMPA‐induced striatal damage. Interestingly, QA‐induced current and calcium influx in striatal R6/2 neurons were not decreased. However, R6/2 neurons had a better capacity to handle cytoplasmic calcium ([Ca²⁺]_c) overload following QA and could avoid [Ca²⁺]_c deregulation and cell lysis. In addition, basal [Ca²⁺]_c levels were increased five‐fold in striatal R6/2 neurons. This might cause an adaptation of R6 neurons to excitotoxic stress resulting in an up‐regulation of defense mechanisms, including an increased capacity to handle [Ca²⁺]_c overload. However, the increased level of basal [Ca²⁺]_c in the HD mice might also disturb intracellular signalling in striatal neurons and thereby cause neuronal dysfunction and behavioural deficits.