A method for performing intrusion detection on a card reader by comparing intrusion detection measurements, said method comprising: providing a card reader assembly in a housing, the card reader assembly including a card slot for receiving a card to be read, the card slot having contact connectors for making physical contact with a chip in the card wherein the contact connectors are surrounded by intrusion detection electrodes (120, 122, 124); providing a capacitive sensor module for detecting changes in capacitance on the intrusion detection electrodes (120, 122, 124), wherein the intrusion detection electrodes are disposed adjacent to the card slot and coupled to the capacitive sensor module and dedicated to detection of conductive or dielectric objects that cause an imbalance of electrical charges on at least one of the intrusion detection electrodes (120, 122, 124); creating an intrusion detection matrix by transmitting at least one signal pattern from the intrusion detection electrodes (120, 122, 124), receiving at least one response on the intrusion detection electrodes, and storing the at least one response in the intrusion detection matrix to show an initial imbalance of electrical charges on the intrusion detection electrodes (120, 122, 124), the intrusion detection matrix being stored in non-volatile memory that is not erased when the card reader is shut off; performing an intrusion detection procedure by transmitting the at least one signal pattern from the intrusion detection electrodes (120, 122, 124), receiving at least one new response on the intrusion detection electrodes and comparing the at least one new response to the initial imbalance of electrical charges stored in the intrusion detection matrix stored in the non-volatile memory to determine if an object has caused a change in capacitance on the intrusion detection electrodes (120, 122, 124); and performing an action if it is determined that the at least one new response is different from the initial imbalance stored in the intrusion detection matrix the action being selected from the group of actions comprised of taking no action and letting the card reader to continue operating but sending an alert signal, or shutting down the card reader. providing a card reader assembly in a housing, the card reader assembly including a card slot for receiving a card to be read, the card slot having contact connectors for making physical contact with a chip in the card wherein the contact connectors are surrounded by intrusion detection electrodes (120, 122, 124); providing a capacitive sensor module for detecting changes in capacitance on the intrusion detection electrodes (120, 122, 124), wherein the intrusion detection electrodes are disposed adjacent to the card slot and coupled to the capacitive sensor module and dedicated to detection of conductive or dielectric objects that cause an imbalance of electrical charges on at least one of the intrusion detection electrodes (120, 122, 124); creating an intrusion detection matrix by transmitting at least one signal pattern from the intrusion detection electrodes (120, 122, 124), receiving at least one response on the intrusion detection electrodes, and storing the at least one response in the intrusion detection matrix to show an initial imbalance of electrical charges on the intrusion detection electrodes (120, 122, 124), the intrusion detection matrix being stored in non-volatile memory that is not erased when the card reader is shut off; performing an intrusion detection procedure by transmitting the at least one signal pattern from the intrusion detection electrodes (120, 122, 124), receiving at least one new response on the intrusion detection electrodes and comparing the at least one new response to the initial imbalance of electrical charges stored in the intrusion detection matrix stored in the non-volatile memory to determine if an object has caused a change in capacitance on the intrusion detection electrodes (120, 122, 124); and performing an action if it is determined that the at least one new response is different from the initial imbalance stored in the intrusion detection matrix the action being selected from the group of actions comprised of taking no action and letting the card reader to continue operating but sending an alert signal, or shutting down the card reader.