An approach of implementing X-bar and R control charts as a statistical control tool to monitor changes in the melting profile of fresh and stored flaxseed oils by differential scanning calorimetry (DSC) was used. Phase transition melting profiles were collected after 0, 2, 4, 6 months of storing flaxseed oils, originated from five different cultivars. Four peaks at around -36, -30, -25, -12 °C were identified using the deconvolution analysis procedure, which enabled data to be collected on peak temperature (T), peak height (h) and the peak area (A), as well as the ratio calculated from these parameters. Control charts of DSC parameters, linked to the second peak (h2, A2) and calculated ratios of those parameters showed an increasing or decreasing trend within the storage time, thus were considered to be indicators of oil deterioration. Since DSC parameters related to the first peak (h1, A1) and third peak (h3, A3) remained unchanged within storage, they were established as the markers of flaxseed oil authenticity.