Chromosomal microarray is highly accurate at what it is designed to do, but it has real limitations that every family should understand before testing. On the technical side, the test reliably measures gains and losses of genetic material down to a small, well-defined size threshold, and most major diagnostic laboratories validate this threshold carefully. It generally does not detect a rearrangement where chromosome material has changed position without being gained or lost, it cannot detect a change within a single gene, and it may miss a genetic imbalance that is present in only a small proportion of a person’s cells, a situation called low-level mosaicism. When a chromosomal microarray result does not explain a strong clinical suspicion, exome or genome sequencing is often the recommended next step, since it can pick up the single-gene changes a microarray is not designed to see.

The most important limitation for families to prepare for, however, is the possibility of a result that is not immediately black or white. Because a chromosomal microarray scans the entire genome, it sometimes flags a small gain or loss of genetic material that has never been well studied, and doctors cannot yet say with confidence whether it is a harmless variation or a meaningful one. This is called a variant of uncertain significance. Rates of this kind of result have fallen substantially over the past decade, from roughly 2 to 3 in 100 tests in early studies to under 1 in 100 today, as shared international databases have accumulated enough data to reclassify many of these findings as either clearly harmless or clearly significant, but the possibility has not disappeared entirely, and a small share of uncertain results are revised, in either direction, as laboratories periodically recheck older data.

A chromosomal microarray can also occasionally reveal information a family did not set out to look for, such as a genetic change linked to a condition that only appears later in life, or a finding in a parent who agreed to be tested alongside a child. For all these reasons, genetic counseling before testing, to explain what kinds of results are possible, and after testing, to interpret whatever is found, is considered an essential part of the process rather than an optional add-on.