Atherton and fellow opener Nick Knight batted cautiously as England moved to 142 without loss by tea with Atherton on 83 and Knight on 53.
It was in the final session that the perseverance of the West Indies pace bowlers, on another hot day and in front of a packed crowd, was finally rewarded.
Fast bowler Kenny Benjamin made the initial breakthrough, trapping Knight lbw for 57 when the batsman padded up without offering a stroke.
Benjamin then had John Crawley well caught at slip by Stuart Williams for 14, Atherton was brilliantly run out for 113 and Graham Thorpe fell to a catch by wicketkeeper Courtney Browne off paceman Ian Bishop for 19.
The England openers appeared determined not to waste the chance of batting first on a docile Trent Bridge pitch after Atherton had won the toss and West Indies were without main strike bowler Curtly Ambrose, ruled out with a recurrence of an old shoulder injury.
Both sides were hit by injury. England was denied the use of batsmen Robin Smith and Alec Stewart, while West Indies was without Ambrose, Jimmy Adams and Carl Hooper.
With the teams level 2-2 in the six-match series, both openers were fortunate early. Knight survived a loud lbw appeal and Atherton had an inside edge off Benjamin shave his off-stump and go for four.
With the pitch offering little help to the pace bowlers, leg-spinner Rajindra Dhanraj, replacing Ambrose, was in action 40 minutes before lunch, a rare sight for a West Indies side on the first day of a test match.
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