Though the Standard Model has made accurate predictions and remains the best picture of the elemental workings of particle physics to date, it is still an incomplete theory. There are fundamental physical phenomena observed in nature that the Standard Model has no adequate explanation for. Some of the most important of these unexplained phenomena include the following:

Yes, it may seem so basic that it is surprising, but the Standard Model does not explain gravity. The approach of simply adding a "graviton" as a theoretical gauge boson to account for the mediation of the gravitational force within the Standard Model does not recreate what is observed experimentally without the aide of yet undiscovered modifications to the current Standard Model. This is one of the Standard Model’s most obvious fundamental weaknesses—the Standard Model is widely considered to be irreconcilable with the most successful theory of gravity to date, general relativity.

Cosmological observations tell us the standard model explains a mere 5% of the energy present in the universe. Of the missing 95%, about 27% should be dark matter. Dark matter is a type of matter hypothesized in astronomy and cosmology to account for observable effects that appear to be the result of mass where no such mass is visibly observed—essentially matter that does not interact at all with the electromagnetic force. Dark matter cannot be seen directly with telescopes as it evidently neither emits nor absorbs light or other electromagnetic radiation at any significant level. The existence of dark matter and its properties, however invisible, can be inferred from its obvious gravitational effects on visible matter, radiation, and the large-scale structure of the universe. According to the Planck mission team, dark matter is estimated to constitute 85% of the total matter in the universe, while dark energy plus dark matter constitute 95% of the total content of the universe. Despite data that indicates 85% of the universe is dark matter, the Standard Model does not supply any fundamental particles that are viable dark matter candidates and attempts to explain dark energy in terms of vacuum energy provided by the Standard Model lead to a mismatch of 120 orders of magnitude (10¹²⁰).

According to the conventional Standard Model, neutrinos are massless particles. This is problematic however because neutrino oscillation experiments have shown that neutrinos do have mass. Mass terms for the neutrinos can be updated to standard model by hand (as this website reports), but these updates lead to new theoretical problems. For example, the mass terms need to be so extraordinarily small that it is not clear whether or not neutrino masses would arise in the same way that the masses of other fundamental particles do in the Standard Model—i.e. even the discovery of the Higgs Boson which alleviates this issue in regards to the other massive and non-massive fundamental particles, does not provide satisfactory explanation of neutrino masses because their mass is so slight, yet they do still have mass. To account for neutrino masses via the Higgs Boson requires the strength of neutrino interactions with the Higgs to be at least 12 orders of magnitude (10¹²) weaker than that of the top quark. Few physicists are willing to accept such a diminutive number as a fundamental constant of nature.

As discussed on other pages, CP-symmetry, in accordance with the parameters established by the Standard Model, states that the laws of physics should be the same if a particle is interchanged with its antiparticle, which carries an opposite charge (“charge” or C symmetry), and inverse spatial coordinates ("mirror" or P symmetry). In other words, in a universe of perfect CP Symmetry, all particles and antiparticles would exist in equal proportion so that if the charge and spatial orientation of either were flipped, it would essentially become the other. In such an instance it follows that there should have been a total cancellation of both— because particles and their antiparticles annihilate each other. Despite the fact that the standard model predicts that matter and antimatter should have been created in nearly equal amounts, the universe is primarily made out of matter. The blatant CP-violation we observe all around us, requires a substantial explanation; while instances of symmetry breaking, such as in instances displayed by interactions with the weak force, have been discovered, as of yet there is no solid mechanism to sufficiently to explain the asymmetry we observe by way of the Standard Model.