We have studied CPT violation in neutrino oscillation considering three flavor framework with matter effect. We have constructed a new way to find the oscillation probability incorporating CPT violating terms without any approximation. Then CPT violation with atmospheric neutrinos for a magnetized iron calorimeter detector considering the muons (directly measurable with high resolution) of the charge current events has been studied for zero and nonzero θ 13 values. It is found that a potential bound of δ b 32 ≲ 6 × 10 − 24 GeV at 99% CL can be obtained with 1 Mton.year exposure of this detector; and unlike neutrino beam experiments, there is no possibility to generate ‘fake’ CPT violation due to matter effect with atmospheric neutrinos. The advantages of atmospheric neutrinos to discriminate CPT violation from CP violation and nonstandard interactions are also discussed.
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