Not everyone who puts on running shoes plans to enter the New York Marathon; and rare is the calorie-conscious person who doesn't occasionally fall off the wagon and into a bag of french fries. Nonetheless, it's a fact that Americans are taking better care of themselves, and the Federal Centers for Disease Control can prove it. There are new figures, however, proving that one bad habit has very long-term consequences.

Last week the C.D.C. announced that the mortality rate in the U.S. fell 8 percent between 1979 and 1986, thanks to extraordinary decreases in death rates from coronary heart disease (18 percent) and stroke (26 percent). And while the medical profession deserves some of the credit, most of it belongs to individual Americans, who are more aware of cholesterol levels and blood pressure. Millions have given up smoking. But sadly, the C.D.C. reported, not all have given it up soon enough. Although the smoking rate has been going down steadily, the mortality rate from lung cancer and other smoking-related lung diseases keeps going up.

The death rate from lung cancer rose 15 percent in the same seven-year period; for diseases like bronchitis and emphysema it went up 33 percent. Why? For one thing, it takes awhile for the effects of smoking to show themselves. They will have an impact on mortality right into the 21st century.

But if it is true that lung diseases have a ''longer tail'' than heart disease or stroke, it's also true that the longer one smokes the higher the risk. To quit is to cut that risk. Anybody who says it's ''too late'' to give up smoking is making a mistake - and maybe a fatal one.